The use of sapcpe is mentioned in this SAP note.
1636252 - Installing a 7.20 kernel in SAP Web AS 7.00/7.01/7.10/7.11
The sapcpe program will be called automatically whenever you start the SAP system as the start script does that to ensure that the DIR_EXECUTABLE location to be consistent.
You can trigger the sapcpe program manually and the procedure is mentioned in the above SAP note.
You just need to make sure that there are no left overs from the old version of the kernel.
You can use the sapcontrol to see whether target version of the kernel files are replicated after the kernel update.
sapcontrol -nr 00 -function GetVersionInfo
Note: Replace 00 with the right system number.
RB